From francois.husson at agrocampus-ouest.fr Tue Feb 3 16:02:29 2009 From: francois.husson at agrocampus-ouest.fr (Francois Husson) Date: Tue, 03 Feb 2009 15:02:29 +0000 Subject: Abstract submission deadline for useR! 2009 Message-ID: <49885C85.7010508@agrocampus-ouest.fr> Dear members of the R user community, the submission deadline for useR! 2009 (Rennes, France, July 8 to 10, 2009) is approaching: Submission deadline: 2009-02-27 (and along with that the early registration deadline). We encourage you to give a presentation at the conference and submit an abstract or a poster on topics presenting innovations or exciting applications of R. You can use the conference Web page at http://www.R-project.org/useR-2009/ Invited speakers will include: Adele Cutler, Peter Dalgaard, Jerome H. Friedman, Michael Greenacre, Trevor Hastie, John Storey, Martin Theus. July 7, 2009, half-day tutorials are presented by R experts prior to the conference. The conference web page: http://www.agrocampus-ouest.fr/math/useR-2009/accomodation.html gives a list of hotels and some student rooms (200) are also available on the campus (Rennes will be very busy at the conference time because the cultural event `Festival Les tomb?es de la nuit' will take place at the same time, so we recommend to book as soon as possible). We hope to meet you in Rennes! F. Husson for the organizing committee. From edd at debian.org Mon Feb 23 05:19:29 2009 From: edd at debian.org (Dirk Eddelbuettel) Date: Sun, 22 Feb 2009 22:19:29 -0600 Subject: R/Finance 2009: Applied Finance with R -- Registration now open Message-ID: <18850.9169.960535.118830@ron.nulle.part> R/Finance 2009: Applied Finance with R April 24 & 25, Chicago, IL, US The first annual R/Finance conference for applied finance using R , the premier free software system for statistical computation and graphics, will be held this spring in Chicago, IL, USA on Friday April 24 and Saturday April 25. The two-day conference will cover topics as diverse as portfolio theory, time-series analysis, as well as advanced risk tools, high-performance computing, and econometrics. All will be discussed within the context of using R as a primary tool for financial risk management and trading. Assembled to talk over the two days are some of the industry's most recognizable authorities within the world of R and quantitative finance. R/Finance 2009 is organized by a leading group of R package authors and community contributors, and hosted by the International Center for Futures and Derivatives [ICFD] at the University of Illinois at Chicago. Conference registration is now open. Special advanced registration pricing is available, as well as discounted pricing for academic and student registrations. More details and registration information can be found at the website at http://www.RinFinance.com For the program committee: Gib Bassett, Peter Carl, Dirk Eddelbuettel, John Miller, Brian Peterson, Dale Rosenthal, Jeffrey Ryan -- Three out of two people have difficulties with fractions. From P.Dalgaard at biostat.ku.dk Tue Mar 3 15:29:37 2009 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Tue, 03 Mar 2009 15:29:37 +0100 Subject: REMINDER: DSC 2009 abstract submission before March 15 Message-ID: <49AD3ED1.20504@biostat.ku.dk> Just a friendly reminder that the closing date for abstract submissions for the DSC conference in Copenhagen is next Sunday. See http://www.r-project.org/dsc-2009 Notice that the website has been revised since we decided to engage a professional convention bureau. The good news is that payment by credit card is now possible. The slightly bad news is that there are now two separate registration paths: one for participation and one for abstracts. -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 From P.Dalgaard at biostat.ku.dk Thu Mar 5 16:57:18 2009 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Thu, 05 Mar 2009 16:57:18 +0100 Subject: R 2.9.0 is scheduled for April 17 Message-ID: <49AFF65E.2040407@biostat.ku.dk> This is to announce that we plan to release R version 2.8.0 on Friday, April 17, 2009. Release procedures start Tuesday March 17. The detailed schedule can be found on http://developer.r-project.org The source tarballs will be made available daily (barring build troubles) and the tarballs can be picked up at http://cran.r-project.org/src/base-prerelease/ a little later. Binary builds are expected to appear starting Friday, March 20. For the Core Team Peter Dalgaard -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 From luke at stat.uiowa.edu Fri Mar 6 14:38:27 2009 From: luke at stat.uiowa.edu (luke at stat.uiowa.edu) Date: Fri, 6 Mar 2009 07:38:27 -0600 (CST) Subject: Travel funding for DSC/useR 2009 for young researchers at U.S. institutions Message-ID: *** Travel and Accommodation Support *** Funds from the U.S. National Science Foundation may be available to provide partial support for travel and accommodation for some graduate students and junior faculty at U.S. post-secondary institutions to attend DSC 2009 and useR 2009. If you wish to apply for this support, please send an application to luke at stat.uiowa.edu. Your application should include a brief CV a copy of your abstract if you have submitted a paper or a poster a statement that demonstrates your eligibility, your need for support, and an amount of support requested students should include a brief letter of support from their supervisor faculty or post-doc applicants should include a brief statement about other funding sources The allocation will be based on merit and need; women and minority candidates are encouraged to apply. Applications must be made by March 31 (2009-03-31) and successful applicants will be notified by email soon thereafter. Please visit the conference web pages at http://www.r-project.org/dsc-2009/ and http://www.agrocampus-rennes.fr/math/useR-2009/ for conference details. Best, Luke Tierney -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics and Fax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: luke at stat.uiowa.edu Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu From luke at stat.uiowa.edu Thu Mar 26 15:17:29 2009 From: luke at stat.uiowa.edu (luke at stat.uiowa.edu) Date: Thu, 26 Mar 2009 09:17:29 -0500 (CDT) Subject: Travel funding for DSC/useR 2009 for young researchers at U.S. institutions Message-ID: *** Travel and Accommodation Support *** [Deadline extended to April 15, 2009] Funds from the U.S. National Science Foundation may be available to provide partial support for travel and accommodation for some graduate students and junior faculty at U.S. post-secondary institutions to attend DSC 2009 and useR 2009. If you wish to apply for this support, please send an application to luke at stat.uiowa.edu. Your application should include a brief CV a copy of your abstract if you have submitted a paper or a poster a statement that demonstrates your eligibility, your need for support, and an amount of support requested students should include a brief letter of support from their supervisor faculty or post-doc applicants should include a brief statement about other funding sources The allocation will be based on merit and need; women and minority candidates are encouraged to apply. Applications must be made by April 15 (2009-04-15) and successful applicants will be notified by email soon thereafter. Please visit the conference web pages at http://www.r-project.org/dsc-2009/ and http://www.agrocampus-rennes.fr/math/useR-2009/ for conference details. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics and Fax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: luke at stat.uiowa.edu Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu From P.Dalgaard at biostat.ku.dk Fri Apr 17 10:56:19 2009 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Fri, 17 Apr 2009 10:56:19 +0200 Subject: R 2.9.0 is released Message-ID: <49E84433.2030805@biostat.ku.dk> I've rolled up R-2.9.0.tar.gz a short while ago. This is a development release which contains a number of new features. Also, a number of mostly minor bugs have been fixed. See the full list of changes below. You can get it (later today) from http://cran.r-project.org/src/base/R-2/R-2.9.0.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. In case of impatience, try http://www.biostat.ku.dk/~pd/R-release Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: 70447ae7f2c35233d3065b004aa4f331 INSTALL 433182754c05c2cf7a04ad0da474a1d0 README 4f004de59e24a52d0f500063b4603bcb OONEWS ff4bd9073ef440b1eb43b1428ce96872 ONEWS 7861f511a3f8e8598c9b84d65e93c389 NEWS 7abcbbc7480df75a11a00bb09783db90 THANKS 070cca21d9f8a6af15f992edb47a24d5 AUTHORS a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB eb723b61539feef013de476e68b5c50a COPYING 020479f381d5f9038dcb18708997f5da RESOURCES b96e9596f947794c5628712f8016aa90 FAQ a5b79a2bc1372136cda4674b5f46d146 R-2.9.0.tar.gz a5b79a2bc1372136cda4674b5f46d146 R-latest.tar.gz This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.9.0 SIGNIFICANT USER-VISIBLE CHANGES o expand.grid() by default no longer coerces strings into factors. NEW FEATURES o Package 'Matrix' is now a recommended package contained in the basic R distribution. It provides S4 classes and methods for dense and sparse matrices, often by using the numerical libraries Lapack and from the SuiteSparse collection CHOLMOD, CSparse, and SPQR among others. o pdf() and postscript() gain a 'useKerning' argument to place strings using kerning (which had previously been ignored in display but not in strwidth), based in part on an idea and code from Ei-ji Nakama. The default is TRUE. Kerning involving spaces is now ignored (it was previously only used in the computation of string widths). o seq.default() and seq.int() ensure that the result is within the interval [from, to] even when the last value would previously have been slightly out of range because of the allowance for rounding error in computing the number of elements. o boxplot() gains a simple 'matrix' method, enabling boxplot(mat) instead of boxplot(data.frame(mat)). o zip.file.extract() gains an optional 'dir' argument (but use unzip() instead). o source() with 'encoding' specified (and not as "unknown") marks the encoding of character strings in Latin-1 and UTF-8 locales. o parse(text=z) now marks the encoding of character strings in Latin-1 and UTF-8 locales if 'z' is of known encoding (that is all elements are either ASCII or marked as Latin-1 or UTF-8). o sprintf() does stricter error checking on input formats to avoid passing invalid formats to the OS (which have a tendency to crash under such inputs). o expand.grid() gains a 'stringsAsFactor' argument to ask for automatic conversion of character vectors to factors (which happened for many years but was not previously documented, and is no longer the default). o bxp() now coputes the 'ylim' including the outliers only if 'outline = TRUE'. (Wish of PR#13196) o barplot() gains a 'args.legend' argument. (Wish of PR#13265). o RweaveLatexSetup() now accepts all (and not just some) options passed through from Sweave() o cumsum(x) and cumprod(x) for double precision x now use a long double accumulator where available and so more closely match sum() and prod() in potentially being more accurate. o plot() methods for "stepfun" (and hence "ecdf") gain an 'col' argument, allowing to set all three colors simultaneously. o Iterating over a factor in a for loop now coerces to a character vector (rather than using the integer codes). o data.frame() now recycles columns of list arguments, not just vectors and factors. o plot.ts(plot.type="multiple") now makes use of *.lab and *.axis graphical parameters (wish of PR#13134 and 13135). o Classes can be exported from a name space using the NAMESPACE file directive 'exportClassPattern' which has the same syntax as 'exportPattern'. o strftime() now converts its first argument with as.POSIXlt() and so is no longer an alias for format.POSIXLt. o body<-() now treats list values consistently with other types: they no longer need to be wrapped in a list() call. o option("pdfbrowser") is now set on Windows as well as on Unix-alikes. o object.size() now returns an object of class "object_size" and has a print() method. o [col/row]Sums(), *Means() now have an additional '...' argument, so that they can more easily be turned into generic functions. o Package 'tools' contains dependsOnPkgs() to compute reverse dependencies. o Strict type checking is now turned on: this catches more internal corruptions, and some badly written contributed code. o There are new functions in package 'tcltk', tk_choose.files(), tk_choose.dir() and tk_messageBox(), analogues of functions available on Windows (the last is an analogue of winDialog). o Sys.glob() now does tilde expansion on all platforms. o read.table() and friends gain a 'fileEncoding' argument to make re-encoding of input just a little bit simpler. o grep() gains an 'invert' argument mimicking 'grep -v/--invert'. o strwrap() now allows a separate prefix for the first line. o grep() has a more efficient sibling grepl() that returns a logical vector. o xfig() has new arguments 'defaultFont' and 'textSpecial' contributed by Sebastian Fischmeister. o parse() and parse_Rd() now point to syntax errors in the reported error context, and include the filename and line and column numbers so smart text editors can jump to the error location. o str(<1d-array>) now writes "[1:n(1d)]" instead of the previous less clear "[, 1:n]". o New function testInstalledPackage() in package 'tools' allows the examples (and if they were installed) any package-specific tests to be run on an installed package. testInstalledPackages() can run all the examples and tests in the standard and/or recommended packages. Also testInstalledBasic() can run the basic tests (if installed). o file.copy() now has a 'recursive' argument. o Errors in setOldClass() will cause a previous definition to be restored. o Ambiguities in class inheritance and method selection resulting from duplicates in superclasses are now resolved by requiring (if possible) consistency with all the superclass inheritance. The rules for method selection have been revised to take advantage of the improved ordering. See ?Methods and the reference there related to inheritance. o New function unzip() in package 'utils' to expand or list zip archives. o Replacement functions for class() and oldClass() will unset the S4 bit when the replacement can't be an S4 object; oldClass() will return the S3 class for S4 objects with slot .S3Class. o clip() takes extra steps to avoid the next graphics call resetting the clip region. o New function sample.int() to provide documented access to the internal part of sample() (sampling from seq_len(n)). o New version of withVisible() for better handling of cases like withVisible(eval.parent(....)). Moved to package 'base' with a view to replace .Internal(eval.with.vis) in source() later. o showClass() which is also used to auto-print class definitions, now mentions the package where the class comes from, if there is one. o simulate(obj) now also works for "glm" objects and for weighted fits, thanks in part to contributions from Ben Bolker and Heather Turner. There is now a means to extend the methods available for "glm" objects, as glm families can have an optional 'simulate' component. o S4 classes that inherit from any of the "structure" classes or from "vector" will turn on methods for all the "Ops" group of functions when the package containing the classes is loaded. See class?structure. o A mechanism now allows S4 classes to inherit from object types "environment", "externalptr" and symbol ("name"). See ?setClass. o demo() gains 'echo' and 'ask' arguments, with defaults similar to example(). o library() no longer checks for the packages merged during the re-organization of 1.9.0. o New function poisson.test() in package 'stats' for exact test of rates and rate ratios. o New function isdebugged() indicates whether its argument has the debug flag set or not. o ls.str() [via print method] now also works when some objects in the environment are missing(). o Subsetting S4-objects (without an explicit "[" method) no longer preserves the class in cases like setClass("C", contains="list"); This reverts a "bug fix" activated in R 2.8.0. o .packages() and .find.packages() no longer check the package info for installed packages with dumped metadata, since this was checked when the package was installed. .packages() only considers such packages to be validly installed (any others were installed in a long-obsolete version of R). Both changes speed up searches in libraries of thousands of packages(). o boxplot() uses butt line endings for its median line (suggestion of Uwe Ligges, PR#13553). o S4 objects passed to a non-default S3 method will be converted to a valid S3 object with the S3 class. See the section on inheriting from non-S4 classes in ?Classes. o A new class "nonStructure" has been defined; classes that extend a vector class but that should lose their slots under Math or Ops functions should extend this class. See class?nonStructure. o axis.POSIXct() now plots in the timezone marked for its inputs (if any) rather than in the local time. The latter was a deliberate choice, but is easy to select by removing the 'tzone' attribute. (Suggestion of Dan Kelley.) o A new function classesToAM() returns an adjacency matrix representing the inheritance of the classes specified. Allows better human examination of the patterns, e.g. by using the matrix as input to one of the graph packages (see the documentation). o X11options(antialias = "none") now works, for consistency with X11(). o sprintf() now allows zero-length arguments (with a zero-length result). (Suggestion of Bill Dunlap.) o unlink() is now able to remove broken symbolic links on Unix-alikes. o New selectSuperClasses() utility. o HoltWinters() now allows parameters alpha and beta to be fixed at 0 and hence beta = FALSE and gamma = FALSE are used to specify restricted models. o A new function smoothScatter has been added to package 'graphics'. It is appropriate for very dense scatter plots and uses density estimation and color to reflect density of plotting. DEPRECATED & DEFUNCT o allGenerics() is defunct. o Use of allocVector(CHARSXP ...) is defunct and gives an error. o The compatibility define for graphics structure NewDevDesc in GraphicsDevice.h has been removed. o Support for versioned installs (R CMD INSTALL --with-package-versions and install.packages(installWithVers = TRUE)) has been removed. Packages installed with versioned names will be ignored. o The numeric and power(0.5) forms of argument to make.link() which were deprecated in 2.4.0 are now defunct: use power() directly. o Conversion to Sd and Ssgm by R CMD Rdconv is now defunct. o Support for R --gui=gnome is now defunct (and package gnomeGUI has been withdrwan as it used a long-obsolete version of GNOME). o R CMD SHLIB on Windows will call the first target (not 'all') in Makevars[.win] in future versions: so make 'all' the first target if you have any. UTILITIES o R CMD build now also uses a Makevars[.win] file for cleaning up src/. o R CMD Rd2dvi and R CMD check are now able to cope with Cyrillic characters in UTF-8 if environment variable _R_CYRILLIC_TEX_ is set to a non-empty value and the latex system has suitable fonts (thanks to a hint from Alexey Shipunov). o New function rtags() in package 'utils' that provides etags-like indexing capabilities for R code files. New front-end script R CMD rtags provides an interface to the rtags() function (see R CMD rtags --help for details). o New environment variable R_TEXI2DVICMD to hold the path (if any) to 'texi2dvi' found at configure time: this now provides the default to option("texi2dvi"). o massage-Examples.pl has been replaced by the R function tools:::massageExamples(). o R CMD REMOVE now uses remove.packages() and hence removes all members of a bundle. o R CMD SHLIB is now an R script and has a new option -n aka --dry-run to show what commands would be run. The same code is used on Unix and Windows. o R CMD Rdconv has new options --package and --version to set the corresponding fields in HTML conversion. o R CMD check runs the package tests with a custom startup file, currently containing 'options(useFancyQuotes = FALSE)'. Those tests are run by an R script: using a tests/Makefile (undocumented) no longer works. o R CMD config now knows about DYLIB_EXT and SHLIB_EXT, for use in configure files. o R CMD BATCH has a new option --no-timing to suppress printing out the session timing. o R CMD Rd2dvi can now work on an installed package. o R CMD check no longer loads package 'tcltk' when checking for code problems, so more problems may be reported. o For R CMD SHLIB on Windows the default 'all' target only makes the DLL, and no longer call targets 'before' and 'after'. Rd CONVERSION o Rd files have an optional \Rdversion{} section, which if missing defaults to 1.0. There is support for version 1.1, a slightly modified version with the following changes: - The warnings for \code{} inside example are suppressed. - Whitespace between arguments in \item and \section is accepted without a warning (see below). - $ is treated literally in text, even for latex conversions. - \ is only an escape before % { } \ . - \R, \dots and \ldots can be followed by {}, and it is recommended that they when not followed by whitespace. - The obsolete interpretation of \Alpha etc is no longer done. o Rd conversion now handles ^ ~ < > | correctly in non-code environments (such as \samp), and # and _ even in latex conversion (but $ still needs to be escaped in version 1.0). o Whitespace between first and second arguments is now accepted for \item and \section, e.g. \item{foo} {some value}. Previously arguments after whitespace were silently ignored, and a warning is given for version 1.0 files. o The Rd files created by prompt() and friends are declared to be version 1.1. o \alias now supports the escaping of { as well as of %, and this is recommended. o parse_Rd(), an experimental parser for Rd files, and Rd2txt(), Rd2HTML(), Rd2latex() and Rd2ex(), even more experimental converters, have been added to package 'tools'. o R CMD check runs the package's Rd files through parse_Rd() for a stricter syntax check. This can be suppressed by setting _R_CHECK_RD_PARSE_ to FALSE. o Added markup \verb, which displays like \code, but parses as verbatim text. Currently only supported by parse_Rd() and Rd2HTML(). INSTALLATION o The shell used by the 'R' script and other shell scripts intended to be run directly can be specified at installation time by setting the (precious) configure variable R_SHELL. o libtool has been updated to 2.2.6a. o --with-ICU is now the default: this means that ICU will be used for collation on Mac OS >= 10.4. o make install-tests can be used to install the test files, to allowed an installed version of R to be tested -- see the R-admin manual. This is also supported by the function testInstalledPackages() in package 'tools'. o 'make install' using a parallel make should now work. o 'make check' now always re-makes and re-runs the package examples, which are now collated in the locale's order (and not ASCII order). o configure will now set the default optimization level for gfortran on x86_64 Linux to -O as -O2 has caused problems with gfortran 4.3.x. PACKAGE INSTALLATION o install.packages() is able to infer that repos=NULL was intended from the extension on the file name specified as 'pkgs'. On Mac OS X it now supports local binary packages with .tar.gz extension. Nonetheless .tgz remains the preferred extension and is expected in repositories. It now checks >= version dependencies for dependent packages, and so will install a newer version of a dependency if needed and available on the repositories. The library being installed into is considered when looking for installed packages if it is not already part of .libPaths() (as INSTALL already does). It has a new argument 'Ncpus' to support parallel installs of source packages. o HTML links will be resolved first to the standard packages: this avoids other installed packages diverting help on e.g. qr() and plot() to themselves. The HTML files are only "touched" if they have changed. o A check is done that the R files can be parsed: this both prevents a broken package without lazy-loading from being installed and gives better diagnostics. o install.packages() gains a 'configure.vars' argument, and both this and 'configure.args' get their defaults from options(). o There is a unified R script for INSTALL on both Unix-alike and Windows that takes option names used by either in the past. It adds --no-multiarch to disable building other than the main sub-architecture, and allows multiple instances of --configure-args and --configure-vars (which will be concatenated). New option --install-tests will install any package-specific tests. o Times in the Packaged: and Built: fields are now recorded in UTC, and in most cases in ISO 8601 format. C-LEVEL FACILITIES o A helper function, asCharacterFactor, converts from factors to character vectors. BUG FIXES o The postscript() output for setting text is faster and smaller. o Subsetting a data frame with duplicate column names without selecting columns (e.g. z[i,]) no longer makes the column names unique. This was never documented, but some packages have assumed it. o data.frame() no longer ignores row names on objects if the first name is empty. (PR#13230: this has been the behaviour for a long time, but apparently undocumented.) o deparse(control="S_compatible") now never uses backticks. o X-spline drawing is improved for cases where the control points are located well off the edges of the device. The symptom of this problem is the error "reached MAXNUMPTS". o exists() with mode= "any" will no longer run an active binding's function. o format(c(1 + 2i, NA)) no longer has extraneous space in " NA". o mood.test() could fail in 2.8.x on large samples because of integer overflow. o heatmap() without a dendrogram could fail. (PR#13512) o Checks for missing values will no longer occasionally result in an infinite loop or stack overflow error, depending on the compiler. Active bindings are now always considered to be non-missing. o Rd conversion was not accepting \p (as in \pkg} or (when using Perl 5.10.x) \k (as in \kbd) in any preamble text in a \value{} section, since those are nowadays interpreted by Perl. (PR#13575) o if(as.raw(1)) TRUE now works as expected. (PR#13630) Also, c(as.raw(12), TRUE) or c(raw(3), pi) do. o duplicated(, incomparables = NA) now gives the intended error message. o name handling of as.data.frame() has been sanitized somewhat o Evaluating an assignment expression with a string on the left hand side no longer destructively changes the string to a symbol in the expression. ************************************************** * * * 2.8 SERIES NEWS * * * ************************************************** CHANGES IN R VERSION 2.8.1 patched NEW FEATURES o R CMD check has a new argument '--install-args' to pass command-line arguments to INSTALL. E.g. --install-args="--docs=normal" on Windows if the HTML Help Workshop is not installed. o R-Forge has been added to R_HOME/etc/repositories, so it will be available interactively in setRepositories(). o The compiled loess() code has been updated to the current version of dloess from Netlib. This includes patches from Ben Tyner which correct some errors when degree = 0 and hence solve PR#13570. INSTALLATION o --with-ICU is now supported (and recommended) on Mac OS X using Apple's supplied port. Note however that the locale category LC_COLLATE cannot be changed whilst R is running on Apple's version of ICU. Configure supports a wider range of ICU versions on other OSes: version 3.0 should suffice, and 3.2, 3.8 and 4.0 have been tested. BUG FIXES o grid-based plots no longer reset the base text size to the default 96dpi in cairo-based bitmap devices. o Rd conversion was incorrectly parsing \\\* and \\\{ (and other cases with an odd number of backslashes greater than one). Text conversion of \code{\ etc} was incorrect (a single backslash stands for itself inside \code). \code{} inside \examples{} is now fixed up (but the warning remains, since it will be handled incorrectly in earlier versions of R). o as.matrix.data.frame() could fail if coercion changed the dimension of one of the columns (as e.g. the coercion of a "Surv" object to a character vector does). o When extracting part of a complex list structure using [[]] with a vector index, the extracted part was not marked for duplication on change. (PR#13411) o Assigning an additional element to a pairlist/language element by x[["foo"]] <- value did not name the additional element. o .Call() and .External() were not accepting "NativeSymbolInfo" and "NativeSymbol" objects as claimed. (Patch from Olaf Mersmann.) o codoc() was missing some default value mismatches with unescaped backslashes, e.g. final="\\" needs to be written as final="\\\\" in the Rd file. The reports on values now give strings in the original quoted format (with \ and " escaped). o The $<- method for pairlists (including language objects) failed to duplicate if NAMED was 2. o read.table(blank.lines.skip = FALSE) gave a final empty row on files with less than 5 lines (PR#13433). o Workaround for a bug in some versions of iconv that was seen with output lines of more than 10,000 bytes and with re-encoding requested on an output connection. o The fullrefman.{dvi,pdf} duplicated part I in part II (at least on some systems). o cbind() could crash with a zero-length input and a list result. o pdf(colormodel = "gray") was setting the stroke colour for fills. o file.show() with multiple files would only show multiple copies of the first one. (PR#13469) o formatC(mode = "character") was documented to work, but did not. (PR#13474) o besselI(x,.., expon.scaled=TRUE) now gives accurate results for x < 1e5 whereas it previously underflowed for x >~= 1500. Further, besselJ(x,..) also computes up to 1e5 (instead of 1e4). o str() was incorrectly warning about its option component 'formatNum' set by strOptions(). o nls(algorithm = "port") did not accept the [factor] notation. (PR#13650) o The relational (aka "comparison") operators are now binary, also in a lower level sense, and an expression as "<"(1) is now erronous. o The 'offset' argument for lm() and glm() is not longer documented to be allowed to be of length 1: this has not been true for a long time. o format.info(x) is now also correct when x has no finite content. o predict.lm() now works correctly when the fit had more than one offset (possibly specified both in the formula and as an argument). This function is called by predict.glm(), so the same isses are corrected there. o besselI(x, nu) with nu a negative integer (a singular case) is now correct. (PR#13556) -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 From francois.husson at agrocampus-ouest.fr Thu Apr 30 13:33:02 2009 From: francois.husson at agrocampus-ouest.fr (Francois Husson) Date: Thu, 30 Apr 2009 11:33:02 +0000 Subject: useR! 2009 program available Message-ID: <49F98C6E.1020705@agrocampus-ouest.fr> Dear members of the R user community, I am pleased to inform you that the program of the useR! 2009 conference (Rennes, France, July 8 to 10, 2009) is available online: http://www.agrocampus-ouest.fr/math/useR-2009/program.html You can register from the link below: http://www.agrocampus-ouest.fr/math/useR-2009/formulaires/registration.php The conference web page: http://www.agrocampus-ouest.fr/math/useR-2009/accomodation.html gives a list of hotels and some student rooms (200) are also available on the campus (Rennes will be very busy at the conference time because the cultural event `Festival Les tomb?es de la nuit' will take place at the same time, so we recommend to book as soon as possible). We hope to meet you in Rennes! F. Husson -- Francois Husson Applied Mathematics Department Agrocampus 65 rue de Saint-Brieuc - CS 84215 - 35042 RENNES Tel : 33 (0) 2 23 48 58 86 Fax : 33 (0) 2 23 48 58 71 m?l : husson at agrocampus-ouest.fr http://www.agrocampus-ouest.fr/math/husson useR!2009 : http://www.agrocampus-ouest.fr/math/useR-2009 From P.Dalgaard at biostat.ku.dk Wed May 6 14:36:54 2009 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Wed, 06 May 2009 14:36:54 +0200 Subject: DSC 2009 update, early registration ends May 15 Message-ID: <4A018466.3090109@biostat.ku.dk> As previously announced, the sixth international workshop on Directions in Statistical Computing (DSC2009) will take place at the Center for Health and Society, University of Copenhagen, Denmark, 13th-14th of July 2009. For details, see http://www.R-project.org/dsc-2009. - The paper selection process is now complete and the programme committee have approximately 25 presentations to assemble into an eventual Final Scientific Programme - Professor Tue Tjur from the Copenhagen Business School has been invited to give an opening lecture on statistical computing in the Old Days. (This was the teacher who introduced me to GENSTAT 30 years ago.) - The Social Programme includes an opening mixer at the conference venue on Sunday evening and a Conference dinner on Monday at Fures{\o} Marina. (http://marina-en.dk) - The closing date for early registration has been postponed to May 15. - The registration is now handled by a professional congress bureau. In particular, this means that payment by credit card has become possible. On behalf of the Organizing Committee, Peter Dalgaard -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 From stvjc at channing.harvard.edu Thu May 28 22:14:51 2009 From: stvjc at channing.harvard.edu (Vincent Carey) Date: Thu, 28 May 2009 16:14:51 -0400 Subject: The R Journal volume 1, number 1, now available Message-ID: <2c3c9e80905281314o1af452cp62b6b9da59ab6e3a@mail.gmail.com> On behalf of the editorial team, I am happy to inform you that the first issue of The R Journal is now available: http://journal.r-project.org I would like to thank team members Heather Turner, Peter Dalgaard, and John Fox for extraordinary efforts in producing this first number of the Journal. -- Vincent Carey, PhD Biostatistics, Channing Lab Editor-In-Chief The R Journal (ISSN 2073-4859) From P.Dalgaard at biostat.ku.dk Mon Jun 8 17:40:53 2009 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Mon, 08 Jun 2009 17:40:53 +0200 Subject: DSC 2009, scientific programme Message-ID: <4A2D3105.9000103@biostat.ku.dk> The as-good-as final scientific programme has been posted on the conference website http://www.r-project.org/dsc-2009 The absolutely final date for regular registration is July 5, but earlier registration is preferred and certainly recommended if you wish to book hotels via the conference bureau. On behalf of the Programme and Organizing Committees Peter Dalgaard -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 From P.Dalgaard at biostat.ku.dk Mon Jun 15 16:38:14 2009 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Mon, 15 Jun 2009 16:38:14 +0200 Subject: R 2.9.1 Scheduled for June 26, 2009 Message-ID: <4A365CD6.7050303@biostat.ku.dk> This is to announce that we plan to release R version 2.9.1 on Friday, June 26, 2009. Release procedures start Tuesday, June 16. Those directly involved should review the generic schedule at http://developer.r-project.org/release-checklist.html The source tarballs will be made available daily (barring build troubles) and the tarballs can be picked up at http://cran.r-project.org/src/base-prerelease/ a little later. Binary builds are expected to appear starting Friday June 19 at the latest. For the Core Team Peter Dalgaard -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 From P.Dalgaard at biostat.ku.dk Fri Jun 26 16:20:07 2009 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Fri, 26 Jun 2009 16:20:07 +0200 Subject: R 2.9.1 is released Message-ID: <4A44D917.7070202@biostat.ku.dk> I've rolled up R-2.9.1.tar.gz a few hours ago. This is a maintenance release and fixes a number of mostly minor issues. See the full list of changes below. You can get it from http://cran.r-project.org/src/base/R-2/R-2.9.1.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: 70447ae7f2c35233d3065b004aa4f331 INSTALL 433182754c05c2cf7a04ad0da474a1d0 README 4f004de59e24a52d0f500063b4603bcb OONEWS ff4bd9073ef440b1eb43b1428ce96872 ONEWS 11a746c387c5a94f172a27939b96dd4c NEWS 7abcbbc7480df75a11a00bb09783db90 THANKS 070cca21d9f8a6af15f992edb47a24d5 AUTHORS a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB eb723b61539feef013de476e68b5c50a COPYING 020479f381d5f9038dcb18708997f5da RESOURCES 8ea34a9306ef5cf5dc03b45883586129 FAQ 54a79eebdf0cec3fd2c489fc94d99b00 R-2.9.1.tar.gz 54a79eebdf0cec3fd2c489fc94d99b00 R-latest.tar.gz Here is the relevant part of the NEWS file: CHANGES IN R VERSION 2.9.1 NEW FEATURES o New function anyDuplicated(x) returns 0 (= FALSE) or the index of the first duplicated entry of x. o matplot(), matlines() and matpoints() now also obey a 'lend' argument, determining line end styles. (Wish of PR#13619). o bw.SJ(), bw.bcv() and bw.ucv() now gain an optional 'tol' argument allowing more accurate estimates. o new.packages() no longer regards packages with the same name as a member of an installed bundle as 'new' (this is now consistent with the dependency checks in install.packages()). It no longer reports on partially installed bundles (since members can be updated individually if a bundle is unbundled). o old.packages() and hence updates.packages() will look for updates to members of package bundles before updates to the whole bundle: this allow bundles to be split and installations updated. o nlminb() gives better non-convergence messages in some cases. o S3 method dispatch will support S4 class inheritance for S3 methods, for primitives and via UseMethod(), if the argument S3methods=TRUE is given to setClass(). S4 method dispatch will use S3 per-object inheritance if S3Class() is set on the object. See ?Methods and the paper referenced there. o R CMD INSTALL is more tolerant of (malformed) packages with a 'man' directory but no validly named .Rd files. o R CMD check now reports where options are used that cause some of the checks to be skipped. o RSiteSearch has been updated to be consistent with the new layout of the search site itself, which now includes separate options for vignettes, views, and r-sig-mixed-models, as well as changed names for r-help. (Contributed by Jonathan Baron.) o That R CMD check makes use of a /tests/Examples/-Ex.Rout.save file as a reference result is now documented in 'Writing R Extensions'. DEPRECATED & DEFUNCT o print.atomic() (defunct since 1.9.0) has been removed since it caused confusion for an S4 class union "atomic". o png(type="cairo1") is deprecated -- it was only needed for platforms with 1.0 <= cairo < 1.2. BUG FIXES o The ... argument was not handled properly when ... was found in the enclosure of the current function, rather than in the function header itself. (This caused integrate() to fail in certain cases.) o col2rgb("#00000080", TRUE) would return the background colour. (Reported by Hadley Wickham.) o interaction() now ensures that the levels of the result are unique. o packageDescription() and hence sessionInfo() now report the correct package version also for a non-attached loaded namespace of a version different from the default lib.loc. o smoothScatter() now also works when e.g. xlim[2] < xlim[1]. o Invalid use of sprintf() such as sprintf("%S%") now give an error instead of a segmentation fault, as do very unusual cases such as sprintf("%s", tryCatch(stop(), error=identity)). (It was always documented that misuse could crash R in platform-dependent ways.) o parse_Rd() would mishandle braces when they occurred at the start of a line within an R string in an Rd file (reported by Alex Couture-Beil) or when they occurred in an R comment (reported by Mark Bravington). o readNEWS() missed version numbers with more than one digit. o building R --without-x no longer fails (PR#13665) o printCoefmat(cbind(0,1)) now works too (PR#13677) o bw.SJ(c(1:99, 1e6)) now works too. o Rd2txt() could not handle empty descriptions of items in an Rd file (reported by Mark Bravington), and did not wrap long lists of arguments if they were given in a single item. o stars() would do a partial plot when called with plot = FALSE; it now consistently returns the locations of the stars. o Rd2latex() could not handle empty sections. o old.packages() and hence update.packages() would fail on a repository which contained only one package but with multiple versions of that package. o as.character.Rd() added extra braces when displaying two-argument macros. (Report and fix by Manuel Eugster.) o unsplit() was misbehaving in the case of single-column data frames. (Reported by Will Gray.) o as(I(1), "vector") and similar coercions from objects of "unregistered" S3 classes now work. o srcref records produced by parse() and parse_Rd() did not record the encoding of the source file. (Reported by Romain Francois.) o The X11 version of View() was misbehaving in MBCS locales, and PgUp/PgDn now behave better, thanks to a patch from Ei-ji Nakama. o R CMD check looked at the environment variable PDFLATEX, but as from R 2.8.1 R CMD Rd2dvi used R_PDFLATEXCMD in preference, and that was set by R CMD (and not PDFLATEX). Now R CMD check looks at R_PDFLATEXCMD. o sprintf() now signals an error when the result of single format specification would be longer than the limit (8192 bytes); it would return "somewhat random" results or segfault previously. (PR#13667) Further, arguments of type "language" or "symbol" are no longer allowed, as these, e.g., sprintf("%s", quote(list())), typically lead to unexpected results or hard to understand error messages. o The new (in 2.9.0) 'stringsAsFactors' argument to expand.grid() was not working: it now does work but has default TRUE for backwards compatibility. o tcrossprod(<1d-array>, ) now does work when the arguments are of compatible dimensions. o qbinom() now is accurate also in (large size, small prob) cases. (PR#13711) o The calculation of the Spearman p-value in cor.test() is slightly more accurate in some cases. (PR#13574) o The digamma(), trigamma() and psigamma() functions could be inaccurate for values of x around 1e-15 due to cancellation. (PR#13714). o median.default() was altered in 2.8.1 to use sum() rather than mean(), although it was still documented to use mean(). This caused problems for POSIXt objects, for which mean() but not sum() makes sense, so the change has been reverted. o Assigning an extra 0-length column to a data frame by DF$foo <- value gave a corrupt data frame rather than failing. (PR#13724) This also happened for DF[["foo"]] <- value. o R CMD INSTALL no longer gives a spurious warning about old R versions ignoring multiple dependencies, if the conditions are known to be satisfied. o The test for setting dim() allowed a value with two or more NAs to be set on a 0-length object. (PR#13729) Also, it allowed an even number of negative values. o xtfrm(), rank(), sort() and order() did not always make use of custom comparison methods specific to the class of elements being sorted. o Increase NAMED value on 'seq' value in for() loop so loop code cannot modify 'seq' value. o Prevent rectangles of size < 0.5 pixel from disappearing in Quartz when using rastered backend. (PR#13744) o Printing _NA_complex_ had a low-level thinko; patch thanks to Bill Dunlap. o CP1257 encoding for postscript/PDF has been corrected. (PR#13736) o aov() with an error term was evaluating the ... arguments in 2.9.0 whilst checking their names, so could fail by evaluating them in the wrong place. (PR#13733) o The print() method for arima() failed if all coefs were fixed. o R CMD INSTALL --no-latex was not implemented in 2.9.0 (only). o Added a needed PROTECT call in RunFinalizers to handle cases where the routine is called recursively from a GC in a finalizer. o Constructing error messages about unused arguments in calls to closures no longer evaluates the arguments. o qr(x, LAPACK=TRUE) did not coerce integer x to numeric. o qr.coef() misbehaved in the LAPACK case with a matrix RHS, so that solve(qr(x, LAPACK=TRUE)) gave wrong results. (Found by Avraham Adler, PR#13762 by Ravi Varadhan.) -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 From katharine.mullen at nist.gov Mon Jul 27 16:02:58 2009 From: katharine.mullen at nist.gov (Mullen, Katharine Megan) Date: Mon, 27 Jul 2009 10:02:58 -0400 Subject: useR! 2010 Message-ID: We are happy to announce that the R user conference useR! 2010 is scheduled for July 21-23, 2010, and will take place at the campus of the National Institute of Standards and Technology (NIST) in Gaithersburg, Maryland, USA. As for the predecessor conferences, the program will consist of two parts: invited lectures and user-contributed sessions (abstract submission will be available online starting from October 2009). Prior to the conference, there will be tutorials on R (proposals for tutorials should be sent before 2009-11-01). INVITED LECTURES Invited speakers will include Mark Handcock, Frank Harrell Jr, Friedrich Leisch, Michael Meyer, Richard Stallman, Luke Tierney, Diethelm Wuertz. USER-CONTRIBUTED SESSIONS The sessions will be a platform to bring together R users, contributors, package maintainers and developers in the S spirit that `users are developers'. People from different fields will show us how they solve problems with R in fascinating applications. The sessions are organized by members of the program committee, including Dirk Eddelbuettel, John Fox, Virgilio Gomez-Rubio, Richard Heiberger, Torsten Hothorn, Aaron King, Jan de Leeuw, Nicholas Lewin-Koh, Andy Liaw, Uwe Ligges, Martin Maechler, Katharine Mullen, Heather Turner, Ravi Varadhan, H. D. Vinod, John Verzani, Alan Zaslavsky, Achim Zeileis. The program will cover topics such as * Applied Statistics & Biostatistics * Bayesian Statistics * Bioinformatics * Chemometrics and Computational Physics * Data Mining * Econometrics & Finance * Environmetrics & Ecological Modeling * High Performance Computing * Machine Learning * Marketing & Business Analytics * Psychometrics * Robust Statistics * Social network analysis * Spatial Statistics * Statistics in the Social and Political Sciences * Teaching * Visualization & Graphics * and many more. PRE-CONFERENCE TUTORIALS Before the official program, half-day tutorials will be offered on Tuesday, July 20th. We invite R users to submit proposals for three hour tutorials on special topics on R. The proposals should give a brief description of the tutorial, including goals, detailed outline, justification why the tutorial is important, background knowledge required and potential attendees. The proposals should be sent before 2009-11-01 to useR-2010 at R-project.org. CONFERENCE WEBPAGE A webpage offering more information is available at http://www.R-project.org/useR-2010 IMPORTANT DATES 2009-10-01 open submission of abstracts 2009-10-01 open registration 2009-11-01 tutorial submission deadline 2010-03-01 early registration deadline 2010-03-01 submission deadline for abstracts Before 2010-03-15 notification of acceptance 2010-06-20 registration deadline (later registration NOT possible on site) 2010-07-20 tutorials 2010-07-21 conference start 2010-07-23 conference end We hope to meet you in Gaithersburg! The organizing committee: Nathan Dodder, William Guthrie, Walter Liggett, John Lu, Katharine Mullen, Jonathon Phillips, Antonio Possolo, Ravi Varadhan. From p.dalgaard at biostat.ku.dk Fri Aug 14 08:00:03 2009 From: p.dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Fri, 14 Aug 2009 08:00:03 +0200 Subject: R 2.9.2 Scheduled for August 24, 2009 Message-ID: <4A84FD63.5010607@biostat.ku.dk> This is to announce that we plan to release R version 2.9.2 on Monday, August 24, 2009. Release procedures start Friday, August 14. Those directly involved should review the generic schedule at http://developer.r-project.org/release-checklist.html The source tarballs will be made available daily (barring build troubles) and the tarballs can be picked up at http://cran.r-project.org/src/base-prerelease/ a little later. Binary builds are expected to appear starting Monday August 17 at the latest. For the Core Team Peter Dalgaard -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 From P.Dalgaard at biostat.ku.dk Mon Aug 24 10:28:02 2009 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Mon, 24 Aug 2009 10:28:02 +0200 Subject: R 2.9.2 is released Message-ID: <4A924F12.3070101@biostat.ku.dk> I've rolled up R-2.9.2.tar.gz a short while ago. This is a maintenance release and fixes a number of mostly minor issues. See the full list of changes below. You can get it from http://cran.r-project.org/src/base/R-2/R-2.9.2.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course (Duncan Murdoch is out of town, so Windows binaries may take a few days longer than usual). For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: 70447ae7f2c35233d3065b004aa4f331 INSTALL 433182754c05c2cf7a04ad0da474a1d0 README 4f004de59e24a52d0f500063b4603bcb OONEWS ff4bd9073ef440b1eb43b1428ce96872 ONEWS 17cbe5399dc80f39bd8c8b3c244d6a50 NEWS 7abcbbc7480df75a11a00bb09783db90 THANKS 070cca21d9f8a6af15f992edb47a24d5 AUTHORS a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB eb723b61539feef013de476e68b5c50a COPYING 020479f381d5f9038dcb18708997f5da RESOURCES 4767b922bb20620946ee9a4275a6ee6c FAQ 112e2a1306cf71320e45d14e87e5b913 R-2.9.2.tar.gz 112e2a1306cf71320e45d14e87e5b913 R-latest.tar.gz Here is the relevant part of the NEWS file: CHANGES IN R VERSION 2.9.2 NEW FEATURES o install.packages(NULL) now lists packages only once even if they occur in more than one repository (as the latest compatible version of those available will always be downloaded). o approxfun() and approx() now accept a 'rule' of length two, for easy specification of different interpolation rules on left and right. They no longer segfault for invalid zero-length specification of 'yleft, 'yright', or 'f'. o seq_along(x) is now equivalent to seq_len(length(x)) even where length() has an S3/S4 method; previously it (intentionally) always used the default method for length(). o PCRE has been updated to version 7.9 (for bug fixes). o agrep() uses 64-bit ints where available on 32-bit platforms and so may do a better job with complex matches. (E.g. PR#13789, which failed only on 32-bit systems.) DEPRECATED & DEFUNCT o R CMD Rd2txt is deprecated, and will be removed in 2.10.0. (It is just a wrapper for R CMD Rdconv -t txt.) o tools::Rd_parse() is deprecated and will be removed in 2.10.0 (which will use only Rd version 2). BUG FIXES o parse_Rd() still did not handle source reference encodings properly. o The C utility function PrintValue no longer attempts to print attributes for CHARSXPs as those attributes are used internally for the CHARSXP cache. This fixes a segfault when calling it on a CHARSXP from C code. o PDF graphics output was producing two instances of anything drawn with the symbol font face. (Report from Baptiste Auguie.) o length(x) <- newval and grep() could cause memory corruption. (PR#13837) o If model.matrix() was given too large a model, it could crash R. (PR#13838, fix found by Olaf Mersmann.) o gzcon() (used by load()) would re-open an open connection, leaking a file descriptor each time. (PR#13841) o The checks for inconsistent inheritance reported by setClass() now detect inconsistent superclasses and give better warning messages. o print.anova() failed to recognize the column labelled P(>|Chi|) from a Poisson/binomial GLM anova as a p-value column in order to format it appropriately (and as a consequence it gave no significance stars). o A missing PROTECT caused rare segfaults during calls to load(). (PR#13880, fix found by Bill Dunlap.) o gsub() in a non-UTF-8 locale with a marked UTF-8 input could in rare circumstances overrun a buffer and so segfault. o R CMD Rdconv --version was not working correctly. o Missing PROTECTs in nlm() caused "random" errors. (PR#13381 by Adam D.I. Kramer, analysis and suggested fix by Bill Dunlap.) o Some extreme cases of pbeta(log.p = TRUE) are more accurate (finite values < -700 rather than -Inf). (PR#13786) pbeta() now reports on more cases where the asymptotic expansions lose accuracy (the underlying TOMS708 C code was ignoring some of these, including the PR#13786 example). o new.env(hash = TRUE, size = NA) now works the way it has been documented to for a long time. o tcltk::tk_choose.files(multi = TRUE) produces better-formatted output with filenames containing spaces. (PR#13875) o R CMD check --use-valgrind did not run valgrind on the package tests. o The tclvalue() and the print() and as.xxx methods for class "tclObj" crashed R with an invalid object -- seen with an object saved from an earlier session. o R CMD BATCH garbled options -d (useful for valgrind, although --debugger=valgrind always worked) o INSTALL with LazyData and Encoding declared in DESCRIPTION might have left options("encoding") set for the rest of the package installation. -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 From P.Dalgaard at biostat.ku.dk Fri Sep 25 12:25:18 2009 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Fri, 25 Sep 2009 12:25:18 +0200 Subject: R 2.10.0 is scheduled for October 26 Message-ID: <4ABC9A8E.7070206@biostat.ku.dk> This is to announce that we plan to release R version 2.10.0 on Monday, October 26, 2009. Release procedures start today. The detailed schedule can be found on http://developer.r-project.org The source tarballs will be made available daily (barring build troubles), starting September 28, and the tarballs can be picked up at http://cran.r-project.org/src/base-prerelease/ a little later. Binary builds are expected to appear soon thereafter. For the Core Team Peter Dalgaard -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 From kmullen at nist.gov Mon Oct 19 04:57:21 2009 From: kmullen at nist.gov (Katharine Mullen) Date: Sun, 18 Oct 2009 22:57:21 -0400 (EDT) Subject: useR! 2010: submission & registration started! Message-ID: We are happy to inform you that abstract submission and registration for `useR! 2010' is now available online from http://www.R-project.org/useR-2010/ This meeting of the R user community will take place at the Gaithersburg, Maryland, USA campus of the National Institute of Standards and Technology (NIST), July 21-23, 2010. The conference schedule is comprised of invited lectures and user-contributed sessions as well as half-day tutorials presented by R experts on July 20, 2010, prior to the conference. Invited speakers will include Mark Handcock, Frank Harrell Jr, Friedrich Leisch, Michael Meyer, Richard Stallman, Luke Tierney, Diethelm Wuertz. We invite you to submit abstracts on topics presenting innovations or exciting applications of R. The call for papers along with the link for abstract submission is available at http://www.R-project.org/useR-2010/#Call ****************************************************************************** Reminder: tutorial proposals are due by November 1, 2009, as specified in the call for tutorials available at http://www.R-project.org/useR-2010/tutorials/ ****************************************************************************** We hope to meet you in Gaithersburg! The organizing committee, Kevin Coakley, Nathan Dodder, David Gil, William Guthrie, Walter Liggett, John Lu, Katharine Mullen, Jonathon Phillips, Antonio Possolo, Ravi Varadhan. From P.Dalgaard at biostat.ku.dk Mon Oct 26 16:20:58 2009 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Mon, 26 Oct 2009 16:20:58 +0100 Subject: R 2.9.0 is released Message-ID: <4AE5BE5A.7000103@biostat.ku.dk> I've rolled up R-2.10.0.tar.gz some hours ago. This is a development release which contains a number of new features, notably a brand new HTML based dynamic help system. Also, a number of mostly minor bugs have been fixed. See the full list of changes below. You can get it from http://cran.r-project.org/src/base/R-2/R-2.10.0.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: 70447ae7f2c35233d3065b004aa4f331 INSTALL 433182754c05c2cf7a04ad0da474a1d0 README 4f004de59e24a52d0f500063b4603bcb OONEWS ff4bd9073ef440b1eb43b1428ce96872 ONEWS b80eafe743ef130e129c6d004793492f NEWS 7abcbbc7480df75a11a00bb09783db90 THANKS 070cca21d9f8a6af15f992edb47a24d5 AUTHORS a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB eb723b61539feef013de476e68b5c50a COPYING 020479f381d5f9038dcb18708997f5da RESOURCES 9ec5df24a0d6ecb04a9817275b825027 FAQ 4486934883b1dbcd5400135e22b26a75 R-2.10.0.tar.gz 4486934883b1dbcd5400135e22b26a75 R-latest.tar.gz This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.10.0 SIGNIFICANT USER-VISIBLE CHANGES o Package help is now converted from Rd by the R-based converters that were first introduced in 2.9.0. This means - Packages that were installed by R-devel after 2009-08-09 should not be used with earlier versions of R, and most aspects of package help (including the runnable examples) will be missing if they are so used. - Text, HTML and latex help and examples for packages installed under the new system are converted on-demand from stored parsed Rd files. (Conversions stored in packages installed under R < 2.10.0 are used if no parsed Rd files are found. It is recommended that such packages be re-installed.) o HTML help is now generated dynamically using an HTTP server running in the R process and listening on the loopback interface. - Those worried about security implications of such a server can disable it by setting the environment variable R_DISABLE_HTTPD to a non-empty value. This disables help.start() and HTML help (so text help is shown instead). - The Java/Javascript search engine has been replaced by an HTML interface to help.search(). help.start() no longer has an argument 'searchEngine' as it is no longer needed. - The HTML help can now locate cross-references of the form \link[pkg]{foo} and \link[pkg:foo]{bar} where 'foo' is an alias in the package, rather than the documented (basename of a) filename (since the documentation has been much ignored). NEW FEATURES o polygon(), pdf() and postscript() now have a parameter 'fillOddEven' (default FALSE), which controls the mode used for polygon fills of self-intersecting shapes. o New debugonce() function; further, getOption("deparse.max.lines") is now observed when debugging, from a code suggestion by John Brzustowski. (PR#13647/8) o plot() methods for "stepfun" and hence "ecdf" no longer plot points by default for n >= 1000. o [g]sub(*, perl=TRUE) now also supports '\E' in order to *end* \U and \L case changes, thanks to a patch from Bill Dunlap. o factor(), `levels<-`(), etc, now ensure that the resulting factor levels are unique (as was always the implied intention). Factors with duplicated levels are still constructible by low-level means, but are now declared illegal. o New print() (S3) method for class "function", also used for auto-printing. Further, .Primitive functions now print and auto-print identically. The new method is based on code suggestions by Romain Fran?ois. o The print() and toLatex() methods for class "sessionInfo" now show the locale in a nicer format and have arguments to suppress locale information. o In addition to previously only round(), there are other 'Math' group (S3) methods for 'difftime', such as floor(), signif(), abs(), etc. o For completeness, old.packages() and available.packages() allow 'type' to be specified (you could always specify 'available' or 'contriburl'). o available.packages() by default only returns information on the latest versions of packages whose version requirements are satisified by the currently running R. o tools::write_PACKAGES() has a new argument 'latestOnly', which defaults to TRUE when only the latest versions in the repository will be listed in the index. o getOption() has a new argument 'default' that is returned if the specified option is not set. This simplifies querying a value and checking whether it is NULL or not. o parse() now warns if the requested encoding is not supported. o The "table" method of as.data.frame() gains a 'stringsAsFactors' argument to allow the classifying factors to be returned as character vectors rather than the default factor type. o If model.frame.default() encounters a character variable where 'xlev' indicates a factor, it now converts the variable to a factor (with a warning). o curve() now returns a list containing the points that were drawn. o spineplot() now accepts axes = FALSE, for consistency with other functions called by plot.factor(). o The Kendall and Spearman methods of cor.test() can optionally use continuity correction when not computing exact p-values. (The Kendall case is the wish of PR#13691.) o R now keeps track of line numbers during execution for code sourced with options(keep.source = TRUE). The source reference is displayed by debugging functions such as traceback(), browser(), recover(), and dump.frames(), and is stored as an attribute on each element returned by sys.calls(). [Experimental] o More functions now have an implicit (S4) generic definition. o quantile.default() now disallows factors (wish of PR#13631) and its help documents what numeric-like properties its input need to have to work correctly. o weighted.mean() is now generic and has "Date", "POSIXct" and "POSIXlt" methods. o Naming subscripts (e.g. x[i=1, j=2]) in data.frame methods for [ and [[ now gives a warning. (Names are ignored in the default method, but could have odd semantics for other methods, and do for the data.frame ones.) o as.data.frame() has an "aovproj" method. (Wish of PR#13505) o as.character(x) for numeric x no longer produces strings such as "0.30", i.e., with trailing zeros. This change also renders levels construction in factor() more consistent. o codocClasses(), which checks consistency of the documentation of S4 class slots, now does so in considerably more cases. The documentation of inherited slots (from superclasses) is now optional. This affects 'R CMD check ' when the package defines S4 classes. o codoc() now also checks S4 methods for code/documentation mismatches. o for(), while(), and repeat() loops now always return NULL as their (invisible) value. This change was needed to address a reference counting bug without creating performance penalties for some common use cases. o The print() method for ls.str() results now obeys an optional 'digits' argument. o The 'method' argument of glm() now allows user-contributed methods. o More general reorder.default() replaces functionality of reorder.factor() and reorder.character(). o The function aspell() has been added to provide an interface to the Aspell spell-checker. o Filters RdTextFilter() and SweaveTeXFilter() have been added to the tools package to provide support for aspell() or other spell checkers. o xtabs() with the new option 'sparse = TRUE' now returns a sparse Matrix, using package 'Matrix'. o contr.sum() etc gain an argument 'sparse' which allows sparse matrices to be returned. contrasts() also gains a 'sparse' argument which it passes to the actual contrast function if that has a formal argument 'sparse'. 'contrasts(f, .) <- val' now also works when 'val' is a sparse Matrix. It is planned that model.matrix() will work with such factors 'f' in the future. o readNEWS() will recognize a UTF-8 byte-order mark (BOM) in the NEWS file. However, it is safer to use only ASCII code there because not all editors recognize BOMs. o New utility function inheritedSlotNames() for S4 class programming. o tabulate() now allows NAs to pass through (and be ignored). o If debug() is called on an S3 generic function then all methods are debugged as well. o Outlier symbols drawn by boxplot() now obey the 'outlwd' argument. Reported by Jurgen Kluge. o svd(x) and eigen(x) now behave analogously to qr(x) in accepting logical matrices x. o File NEWS is now in UTF-8, and has a BOM (often invisible) on the first line, and Emacs local variables set for UTF-8 at the end. RShowDoc("NEWS") should display this correctly, given suitable fonts. o terms.formula(simplify = TRUE) now does not deparse the LHS and so preserves non-standard responses such as `a: b` (requested by Sundar Dorai-Raj). o New function news() for building and querying R or package news information. o z^n for integer n and complex z is more accurate now if |n| <= 65536. o factor(NULL) now returns the same as factor(character(0)) instead of an error, and table(NULL) consequently does analogously. o as.data.frame.vector() (and its copies) is slightly faster by avoiding a copy if there are no names (following a suggestion of Tim Hesterberg). o writeLines(), writeBin() and writeChar() have a new argument 'useBytes'. If false, character strings with marked encodings are translated to the current locale (as before) but if true they are written byte-by-byte. o iconv() has a new argument 'mark' which can be used (by experts) to suppress the declaration of encodings. o DESCRIPTION 'LinkingTo' specs are now recognized as installation dependencies, and included in package management computations. o Standardized DESCRIPTION 'License' specs are now available for package management computations. o "\uxxxx" and "\Uxxxxxxxx" escapes can now be parsed to a UTF-8 encoded string even in non-UTF-8 locales (this has been implemented on Windows since R 2.7.0). The semantics have been changed slightly: a string containing such escapes is always stored in UTF-8 (and hence is suitable for portably including Unicode text in packages). o New as.raw() method for "tclObj" objects (wish of PR#13578). o Rd.sty now makes a better job of setting email addresses, including using a monospaced font. o textConnection() gains an 'encoding' argument to determine how input strings with marked encodings will be handled. o R CMD Rd2pdf is available as a shortcut for R CMD Rd2dvi --pdf. o R CMD check now checks links where a package is specified (\link[pkg]{file} or \link[pkg:file]{topic}), if the package is available. It notes if the package is not available, as in many cases this is an error in the link. o identical() gains three logical arguments, which allow for even more differentiation, notably '-0' and '0'. o legend() now can specify the 'border' color of filled boxes, thanks to a patch from Frederic Schutz. o Indexing with a vector index to [[]] has now been extended to all recursive types. o Pairlists may now be assigned as elements of lists. (Lists could always be created with pairlist elements, but [[<- didn't support assigning them.) o The parser now supports C-preprocessor-like #line directives, so error messages and source references may refer to the original file rather than an intermediate one. o New functions findLineNum() and setBreakpoint() work with the source references to find the location of source lines and set breakpoints (using trace()) at those lines. o Namespace importing is more careful about warning on masked generics, thanks to a patch by Yohan Chalabi. o detach() now has an argument 'character.only' with the same meaning as for library() or require(). o available.packages() gains a 'filters' argument for specifying the filtering operations performed on the packages found in the repositories. A new built-in 'license/FOSS' filter only retains packages for which installation can proceed solely based on packages which can be verified as Free or Open Source Software (FOSS) employing the available license specifications. o In registering an S3 class by a call to setOldClass(), the data part (e.g., the object type) required for the class can be included as one of the superclasses in the Classes argument. o The argument 'f' to showMethods() can be an expression evaluating to a generic function, allowing methods to be shown for non-exported generics and other nonstandard cases. o sprintf() now supports '%o' for octal conversions. o New function Sys.readlink() for information about symbolic links, including if a file is a symbolic link. o Package 'tools' has new functions checkRdaFiles() and resaveRdaFiles() to report on the format of .rda/.RData data files, and to re-save them in a different compressed format, including choosing the most compact format available. A new INSTALL option, --resave-data, makes use of this. o File ~/.R/config is used in preference to ~/.Rconfig, and these are now documented in 'R Installation and Administration'. o Logic operations with complex numbers now work, as they were always documented to, and as in S. o arrows() and segments() allow one of x1 or y1 to be omitted to simplify the specification of vertical or horizontal lines (suggestion of Tim Hesterberg). o approxfun() is faster by avoiding repeated NA checks (diagnosis and patch by Karline Soetaert & Thomas Petzoldt). o There are the beginnings of a Nynorsk translation by Karl Ove Hufthammer. o stripchart() allows par 'bg' to be passed in for the background colour for pch = 21 (wish of PR#13984). o New generic function .DollarNames() to enable class authors to customize completion after the $ extractor. o load(), save(), dput() and dump() now open a not-yet-open connection in the appropriate mode (as other functions using connections directly already did). REGULAR EXPRESSIONS o A different regular expression engine is used for basic and extended regexps and is also for approximate matching. This is based on the TRE library of Ville Laurikari, a modifed copy of which is included in the R sources. This is often faster, especially in a MBCS locale. Some known differences are that it is less tolerant of invalid inputs in MBCS locales, and in its interpretation of undefined (extended) regexps such as "^*". Also, the interpretation of ranges such as [W-z] in caseless matching is no longer to map the range to lower case. This engine may in future be used in 'literal' mode for fixed = TRUE, and there is a compile-time option in src/main/grep.c to do so. o The use of repeated boundary regexps in gsub() and gregexpr() as warned about in the help page does not work in this engine (it did in the previous one since 2005). o Extended (and basic) regexps now support same set of options as for fixed = TRUE and perl = TRUE, including 'useBytes' and support for UTF-8-encoded strings in non-UTF-8 locales. o agrep() now has full support for MBCS locales with a modest speed penalty. This enables help.search() to use approximate matching character-wise rather than byte-wise. o [g]sub use a single-pass algorithm instead of matching twice and so is usually faster. o The perl = TRUE versions now work correctly in a non-UTF-8 MBCS locale, by translating the inputs to UTF-8. o useBytes = TRUE now inhibits the translation of inputs with marked encodings. o strsplit() gains a 'useBytes' argument. o The algorithm used by strsplit() has been reordered to batch by elements of 'split': this can be much faster for fixed = FALSE (as multiple compilation of regexps is avoided). o The help pages, including ?regexp, have been updated and should be consulted for details of the new implementations. HELP & Rd FILE CHANGES o A new dynamic HTML help system is used by default, and may be controlled using tools::startDynamicHelp(). With this enabled, HTML help pages will be generated on request, resolving links by searching through the current .libPaths(). The user may set option("help.ports") to control which IP port is used by the server. o help.start() no longer sets options(htmlhelp = TRUE) (it used to on Unix but not on Windows). Nor does it on Unix reset the "browser" option if given an argument of that name. Arguments 'update' and 'remote' are now available on all platforms: the default is update = FALSE since the http server will update the package index at first use. o help() has a new argument 'help_type' (with default set by the option of that name) to supersede 'offline', 'htmlhelp' and 'chmhelp' (although for now they still work if 'help_type' is unset). There is a new type, "PDF" to allow offline PDF (rather than PostScript). A function offline_help_helper() will be used if this exists in the workspace or further down the search path, otherwise the function of that name in the 'utils' name space is used. o Plain text help is now used as the fallback for HTML help (as it always was for Compiled HTML help on Windows). o It is possible to ask for static HTML pages to be prebuilt via the configure option --enable-prebuilt-html. This may be useful for those who wish to make HTML help available outside R, e.g. on a local web site. o An experimental tag \Sexpr has been added to Rd files, to evaluate expressions at build, install, or render time. Currently install time and render time evaluation are supported. o Tags \if, \ifelse and \out have been added to allow format-specific (or more general, using \Sexpr) conditional text in man pages. o The parse_Rd() parser has been made more tolerant of coding errors in Rd files: now all syntax errors are reported as warnings, and an attempt is made to continue parsing. o parse_Rd() now has an argument 'fragment' (default FALSE) to accept small fragments of Rd files (so that \Sexpr can output Rd code which is then parsed). o parse_Rd() now always converts its input to UTF-8. The Rd2* rendering functions have a new parameter, 'outputEncoding', which controls how their output is encoded. o parse_Rd() no longer includes the newline as part of a "%"-style comment. o There have been various bug fixes and code reorganization in the Rd renderers Rd2HTML, Rd2latex, Rd2txt, and Rd2ex. All example files are now created with either ASCII or UTF-8 encoding, and the encoding is only marked in the file if there is any non-UTF-8 code (previously it was marked if the help file had non-ASCII contents, possibly in other sections). o print.Rd() now adds necessary escape characters so that printing and re-parsing an Rd object should produce an equivalent object. o parse_Rd() was incorrectly handling multiple backslashes in R code strings, converting 4n+3 backslashes to 2n+1 instead of 2n+2. o parse_Rd() now recognizes the \var tag within a quoted string in R-like text. o parse_Rd() now treats the argument of \command as LaTeX-like, rather than verbatim. COMPRESSION o New function untar() to list or unpack tar archives, possibly compressed. This uses either an external 'tar' command or an internal implementation. o New function tar() to create (possibly compressed) tar archives. o New functions memCompress() and memDecompress() for in-memory compression and decompression. o bzfile() has a 'compress' argument to select the amount of effort put into compression when writing. o New function xzfile() for use with xz-compressed files. (This can also read files compressed by some versions of 'lzma'.) o gzfile() looks at the file header and so can now also read bzip2-ed files and xz-compressed files. o There are the new options of save(compress = "bzip2") and "xz" to use bzip2 or xz compression (which will be slower, but can give substantially smaller files). Argument compression_level gives finer control over the space/time tradeoffs. load() can read such saves (but only as from this version of R). o R CMD INSTALL/check and tools::writePACKAGES accept a wider range of compressed tar archives. Precisely how wide depends on the capabilities of the host system's 'tar' command: they almost always include .tar.bz2 archives, and with modern versions of 'tar' other forms of compression such as lzma and xz, and arbitrary extensions. o R CMD INSTALL has a new option --data-compress to control the compression used when lazy-loading data. New possibilities are --data-compress=bzip2 which will give ca 15% better compression at the expense of slower installation times, and --data-compress=xz, often giving even better compression on large datasets at the expense of much longer installation times. (The latter is used for the recommended packages: it is particularly effective for 'survival'.) o file() for open = "", "r" or "rt" will automagically detect compressed files (from gzip, bzip2 or xz). This means that compressed files can be specified by file name (rather than via a gzfile() connection) to read.table(), readlines(), scan() and so on. o data() can handle compressed text files with extensions .{txt,tab,csv}.{gz,bz2,xz} . DEPRECATED & DEFUNCT o png(type="cairo1") is defunct: the value is no longer recognized. o tools::Rd_parse() is defunct (as this version of R uses only Rd version 2). o Use of ~/.Rconf (which was deprecated in favour of ~/.Rconfig in 2004) has finally been removed. o Bundles of packages are deprecated. See 'Writing R Extensions' for the steps needed to unbundle a bundle. o help() arguments 'offline', 'htmlhelp' and 'chmhelp' are deprecated in favour of 'help_type'. o clearNames() ('stats') is deprecated for unname(). o Basic regular expressions (extended = FALSE) are deprecated in strsplit, grep and friends. There is a precise POSIX standard for them, but it is not what recent RE engines implement, and it seems that in almost all cases package authors intended fixed = TRUE when using extended = FALSE. o methods::trySilent() is deprecated for try(*, silent=TRUE) or - more efficiently and flexibly - something like tryCatch(*, error = function(e) e). o index.search() is deprecated: there are no longer directories of types other than 'help'. INSTALLATION o cairo >= 1.2 is now required (1.2.0 was released in July 2006) for cairo-based graphics devices (which remain optional). o A suitable iconv() is now required: support for configure option --without-iconv has been withdrawn (it was deprecated in R 2.5.0). o Perl is no longer 'essential'. R can be built without it, but scripts R CMD build, check, Rprof and Sd2d require it. o A system 'glob' function is now essential (a working Sys.glob() has been assumed since R 2.9.0 at least). o C99 support for MBCS is now required, and configure option --disable-mbcs has been withdrawn. o Having a version of 'tar' capable of automagically detecting compressed archives is useful for utils::untar(), and so 'gtar' (a common name for GNU tar) is preferred to 'tar': set environment variable TAR to specify a particular 'tar' command. INTERNATIONALIZATION o There is some makefile support for adding/updating translations in packages: see po/README and 'Writing R Extensions'. There is support for the use of 'dngettext' for C-level translations in packages: see 'Writing R Extensions'. BUG FIXES o Assigning an extra 0-length column to a data frame by DF[, "foo"] <- value now works in most cases (by filling with NAs) or fails. (It used to give a corrupt data frame.) o validObject() avoids an error during evaluation in the case of various incorrect slot definitions. o n:m now returns a result of type "integer" in a few more boundary cases. o The 'zap.ind' argument to printCoefmat() did not usually work as other code attempted to ensure that non-zero values had a non-zero representation. o printCoefmat() formatted groups of columns together, not just the cs.ind group but also the zap.ind group and a residual group. It now formats all columns except the cs.ind group separately (and zaps the zap.ind group column-by-column). The main effect will be see in the output from print.anova, as this grouped SS-like columns in the zap.ind group. o R_ReplDLLinit() initializes the top-level jump so that some embedded applications on Windows no longer crash on error. o identical() failed to take the encoding of character strings into account, so identical byte patterns are not necessarily identical strings, and similarly Latin-1 and UTF-8 versions of the same string differ in byte pattern. o methods(f) used to warn unnecessarily for an S4 generic 'f' which had been created based on an existing S3 generic. o The check for consistent ordering of superclasses was not ignoring all conditional relations (the symptom was usually spurious warnings for classes extending "array"). o Trying to assign into a raw vector with an index vector containing NAs could cause a segfault. Reported by Herv? Pag?s. o Rscript could segfault if (by user error) its filename argument was missing. Reported by Martin Morgan. o getAnywhere() (and functions that use it, including argument completion in the console) did not handle special built-in functions. Reported by Romain Francois. o order() was missing a PROTECT() call and so could segfault when called on character data under certain (rare) circumstances involving marked non-native encodings. o prettyNum(z, drop0trailing=TRUE) did not work correctly when z was a complex vector. Consequently, str(z, ...) also did not. (PR#13985) o 'make distclean' removed too many files in etc/ if builddir = srcdir. o R CMD replaced TEXINPUTS rather than appending to it (as documented and intended). o help.start() no longer fails on unix when "browser" is a function. o pbeta(x, *, log.p = TRUE) is sometimes more accurate, e.g., for very small x. o Unserializing a pre-2.8 workspace containing pure ASCII character objects with a LATIN1 or UTF-8 encoding would corrupt the CHARSXP cache. -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 From P.Dalgaard at biostat.ku.dk Mon Oct 26 16:29:45 2009 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Mon, 26 Oct 2009 16:29:45 +0100 Subject: R 2.10.0 is released Message-ID: <4AE5C069.7020403@biostat.ku.dk> (D'oh. Forgot to change the Subject: line...) I've rolled up R-2.10.0.tar.gz some hours ago. This is a development release which contains a number of new features, notably a brand new HTML based dynamic help system. Also, a number of mostly minor bugs have been fixed. See the full list of changes below. You can get it from http://cran.r-project.org/src/base/R-2/R-2.10.0.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: 70447ae7f2c35233d3065b004aa4f331 INSTALL 433182754c05c2cf7a04ad0da474a1d0 README 4f004de59e24a52d0f500063b4603bcb OONEWS ff4bd9073ef440b1eb43b1428ce96872 ONEWS b80eafe743ef130e129c6d004793492f NEWS 7abcbbc7480df75a11a00bb09783db90 THANKS 070cca21d9f8a6af15f992edb47a24d5 AUTHORS a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB eb723b61539feef013de476e68b5c50a COPYING 020479f381d5f9038dcb18708997f5da RESOURCES 9ec5df24a0d6ecb04a9817275b825027 FAQ 4486934883b1dbcd5400135e22b26a75 R-2.10.0.tar.gz 4486934883b1dbcd5400135e22b26a75 R-latest.tar.gz This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.10.0 SIGNIFICANT USER-VISIBLE CHANGES o Package help is now converted from Rd by the R-based converters that were first introduced in 2.9.0. This means - Packages that were installed by R-devel after 2009-08-09 should not be used with earlier versions of R, and most aspects of package help (including the runnable examples) will be missing if they are so used. - Text, HTML and latex help and examples for packages installed under the new system are converted on-demand from stored parsed Rd files. (Conversions stored in packages installed under R < 2.10.0 are used if no parsed Rd files are found. It is recommended that such packages be re-installed.) o HTML help is now generated dynamically using an HTTP server running in the R process and listening on the loopback interface. - Those worried about security implications of such a server can disable it by setting the environment variable R_DISABLE_HTTPD to a non-empty value. This disables help.start() and HTML help (so text help is shown instead). - The Java/Javascript search engine has been replaced by an HTML interface to help.search(). help.start() no longer has an argument 'searchEngine' as it is no longer needed. - The HTML help can now locate cross-references of the form \link[pkg]{foo} and \link[pkg:foo]{bar} where 'foo' is an alias in the package, rather than the documented (basename of a) filename (since the documentation has been much ignored). NEW FEATURES o polygon(), pdf() and postscript() now have a parameter 'fillOddEven' (default FALSE), which controls the mode used for polygon fills of self-intersecting shapes. o New debugonce() function; further, getOption("deparse.max.lines") is now observed when debugging, from a code suggestion by John Brzustowski. (PR#13647/8) o plot() methods for "stepfun" and hence "ecdf" no longer plot points by default for n >= 1000. o [g]sub(*, perl=TRUE) now also supports '\E' in order to *end* \U and \L case changes, thanks to a patch from Bill Dunlap. o factor(), `levels<-`(), etc, now ensure that the resulting factor levels are unique (as was always the implied intention). Factors with duplicated levels are still constructible by low-level means, but are now declared illegal. o New print() (S3) method for class "function", also used for auto-printing. Further, .Primitive functions now print and auto-print identically. The new method is based on code suggestions by Romain Fran?ois. o The print() and toLatex() methods for class "sessionInfo" now show the locale in a nicer format and have arguments to suppress locale information. o In addition to previously only round(), there are other 'Math' group (S3) methods for 'difftime', such as floor(), signif(), abs(), etc. o For completeness, old.packages() and available.packages() allow 'type' to be specified (you could always specify 'available' or 'contriburl'). o available.packages() by default only returns information on the latest versions of packages whose version requirements are satisified by the currently running R. o tools::write_PACKAGES() has a new argument 'latestOnly', which defaults to TRUE when only the latest versions in the repository will be listed in the index. o getOption() has a new argument 'default' that is returned if the specified option is not set. This simplifies querying a value and checking whether it is NULL or not. o parse() now warns if the requested encoding is not supported. o The "table" method of as.data.frame() gains a 'stringsAsFactors' argument to allow the classifying factors to be returned as character vectors rather than the default factor type. o If model.frame.default() encounters a character variable where 'xlev' indicates a factor, it now converts the variable to a factor (with a warning). o curve() now returns a list containing the points that were drawn. o spineplot() now accepts axes = FALSE, for consistency with other functions called by plot.factor(). o The Kendall and Spearman methods of cor.test() can optionally use continuity correction when not computing exact p-values. (The Kendall case is the wish of PR#13691.) o R now keeps track of line numbers during execution for code sourced with options(keep.source = TRUE). The source reference is displayed by debugging functions such as traceback(), browser(), recover(), and dump.frames(), and is stored as an attribute on each element returned by sys.calls(). [Experimental] o More functions now have an implicit (S4) generic definition. o quantile.default() now disallows factors (wish of PR#13631) and its help documents what numeric-like properties its input need to have to work correctly. o weighted.mean() is now generic and has "Date", "POSIXct" and "POSIXlt" methods. o Naming subscripts (e.g. x[i=1, j=2]) in data.frame methods for [ and [[ now gives a warning. (Names are ignored in the default method, but could have odd semantics for other methods, and do for the data.frame ones.) o as.data.frame() has an "aovproj" method. (Wish of PR#13505) o as.character(x) for numeric x no longer produces strings such as "0.30", i.e., with trailing zeros. This change also renders levels construction in factor() more consistent. o codocClasses(), which checks consistency of the documentation of S4 class slots, now does so in considerably more cases. The documentation of inherited slots (from superclasses) is now optional. This affects 'R CMD check ' when the package defines S4 classes. o codoc() now also checks S4 methods for code/documentation mismatches. o for(), while(), and repeat() loops now always return NULL as their (invisible) value. This change was needed to address a reference counting bug without creating performance penalties for some common use cases. o The print() method for ls.str() results now obeys an optional 'digits' argument. o The 'method' argument of glm() now allows user-contributed methods. o More general reorder.default() replaces functionality of reorder.factor() and reorder.character(). o The function aspell() has been added to provide an interface to the Aspell spell-checker. o Filters RdTextFilter() and SweaveTeXFilter() have been added to the tools package to provide support for aspell() or other spell checkers. o xtabs() with the new option 'sparse = TRUE' now returns a sparse Matrix, using package 'Matrix'. o contr.sum() etc gain an argument 'sparse' which allows sparse matrices to be returned. contrasts() also gains a 'sparse' argument which it passes to the actual contrast function if that has a formal argument 'sparse'. 'contrasts(f, .) <- val' now also works when 'val' is a sparse Matrix. It is planned that model.matrix() will work with such factors 'f' in the future. o readNEWS() will recognize a UTF-8 byte-order mark (BOM) in the NEWS file. However, it is safer to use only ASCII code there because not all editors recognize BOMs. o New utility function inheritedSlotNames() for S4 class programming. o tabulate() now allows NAs to pass through (and be ignored). o If debug() is called on an S3 generic function then all methods are debugged as well. o Outlier symbols drawn by boxplot() now obey the 'outlwd' argument. Reported by Jurgen Kluge. o svd(x) and eigen(x) now behave analogously to qr(x) in accepting logical matrices x. o File NEWS is now in UTF-8, and has a BOM (often invisible) on the first line, and Emacs local variables set for UTF-8 at the end. RShowDoc("NEWS") should display this correctly, given suitable fonts. o terms.formula(simplify = TRUE) now does not deparse the LHS and so preserves non-standard responses such as `a: b` (requested by Sundar Dorai-Raj). o New function news() for building and querying R or package news information. o z^n for integer n and complex z is more accurate now if |n| <= 65536. o factor(NULL) now returns the same as factor(character(0)) instead of an error, and table(NULL) consequently does analogously. o as.data.frame.vector() (and its copies) is slightly faster by avoiding a copy if there are no names (following a suggestion of Tim Hesterberg). o writeLines(), writeBin() and writeChar() have a new argument 'useBytes'. If false, character strings with marked encodings are translated to the current locale (as before) but if true they are written byte-by-byte. o iconv() has a new argument 'mark' which can be used (by experts) to suppress the declaration of encodings. o DESCRIPTION 'LinkingTo' specs are now recognized as installation dependencies, and included in package management computations. o Standardized DESCRIPTION 'License' specs are now available for package management computations. o "\uxxxx" and "\Uxxxxxxxx" escapes can now be parsed to a UTF-8 encoded string even in non-UTF-8 locales (this has been implemented on Windows since R 2.7.0). The semantics have been changed slightly: a string containing such escapes is always stored in UTF-8 (and hence is suitable for portably including Unicode text in packages). o New as.raw() method for "tclObj" objects (wish of PR#13578). o Rd.sty now makes a better job of setting email addresses, including using a monospaced font. o textConnection() gains an 'encoding' argument to determine how input strings with marked encodings will be handled. o R CMD Rd2pdf is available as a shortcut for R CMD Rd2dvi --pdf. o R CMD check now checks links where a package is specified (\link[pkg]{file} or \link[pkg:file]{topic}), if the package is available. It notes if the package is not available, as in many cases this is an error in the link. o identical() gains three logical arguments, which allow for even more differentiation, notably '-0' and '0'. o legend() now can specify the 'border' color of filled boxes, thanks to a patch from Frederic Schutz. o Indexing with a vector index to [[]] has now been extended to all recursive types. o Pairlists may now be assigned as elements of lists. (Lists could always be created with pairlist elements, but [[<- didn't support assigning them.) o The parser now supports C-preprocessor-like #line directives, so error messages and source references may refer to the original file rather than an intermediate one. o New functions findLineNum() and setBreakpoint() work with the source references to find the location of source lines and set breakpoints (using trace()) at those lines. o Namespace importing is more careful about warning on masked generics, thanks to a patch by Yohan Chalabi. o detach() now has an argument 'character.only' with the same meaning as for library() or require(). o available.packages() gains a 'filters' argument for specifying the filtering operations performed on the packages found in the repositories. A new built-in 'license/FOSS' filter only retains packages for which installation can proceed solely based on packages which can be verified as Free or Open Source Software (FOSS) employing the available license specifications. o In registering an S3 class by a call to setOldClass(), the data part (e.g., the object type) required for the class can be included as one of the superclasses in the Classes argument. o The argument 'f' to showMethods() can be an expression evaluating to a generic function, allowing methods to be shown for non-exported generics and other nonstandard cases. o sprintf() now supports '%o' for octal conversions. o New function Sys.readlink() for information about symbolic links, including if a file is a symbolic link. o Package 'tools' has new functions checkRdaFiles() and resaveRdaFiles() to report on the format of .rda/.RData data files, and to re-save them in a different compressed format, including choosing the most compact format available. A new INSTALL option, --resave-data, makes use of this. o File ~/.R/config is used in preference to ~/.Rconfig, and these are now documented in 'R Installation and Administration'. o Logic operations with complex numbers now work, as they were always documented to, and as in S. o arrows() and segments() allow one of x1 or y1 to be omitted to simplify the specification of vertical or horizontal lines (suggestion of Tim Hesterberg). o approxfun() is faster by avoiding repeated NA checks (diagnosis and patch by Karline Soetaert & Thomas Petzoldt). o There are the beginnings of a Nynorsk translation by Karl Ove Hufthammer. o stripchart() allows par 'bg' to be passed in for the background colour for pch = 21 (wish of PR#13984). o New generic function .DollarNames() to enable class authors to customize completion after the $ extractor. o load(), save(), dput() and dump() now open a not-yet-open connection in the appropriate mode (as other functions using connections directly already did). REGULAR EXPRESSIONS o A different regular expression engine is used for basic and extended regexps and is also for approximate matching. This is based on the TRE library of Ville Laurikari, a modifed copy of which is included in the R sources. This is often faster, especially in a MBCS locale. Some known differences are that it is less tolerant of invalid inputs in MBCS locales, and in its interpretation of undefined (extended) regexps such as "^*". Also, the interpretation of ranges such as [W-z] in caseless matching is no longer to map the range to lower case. This engine may in future be used in 'literal' mode for fixed = TRUE, and there is a compile-time option in src/main/grep.c to do so. o The use of repeated boundary regexps in gsub() and gregexpr() as warned about in the help page does not work in this engine (it did in the previous one since 2005). o Extended (and basic) regexps now support same set of options as for fixed = TRUE and perl = TRUE, including 'useBytes' and support for UTF-8-encoded strings in non-UTF-8 locales. o agrep() now has full support for MBCS locales with a modest speed penalty. This enables help.search() to use approximate matching character-wise rather than byte-wise. o [g]sub use a single-pass algorithm instead of matching twice and so is usually faster. o The perl = TRUE versions now work correctly in a non-UTF-8 MBCS locale, by translating the inputs to UTF-8. o useBytes = TRUE now inhibits the translation of inputs with marked encodings. o strsplit() gains a 'useBytes' argument. o The algorithm used by strsplit() has been reordered to batch by elements of 'split': this can be much faster for fixed = FALSE (as multiple compilation of regexps is avoided). o The help pages, including ?regexp, have been updated and should be consulted for details of the new implementations. HELP & Rd FILE CHANGES o A new dynamic HTML help system is used by default, and may be controlled using tools::startDynamicHelp(). With this enabled, HTML help pages will be generated on request, resolving links by searching through the current .libPaths(). The user may set option("help.ports") to control which IP port is used by the server. o help.start() no longer sets options(htmlhelp = TRUE) (it used to on Unix but not on Windows). Nor does it on Unix reset the "browser" option if given an argument of that name. Arguments 'update' and 'remote' are now available on all platforms: the default is update = FALSE since the http server will update the package index at first use. o help() has a new argument 'help_type' (with default set by the option of that name) to supersede 'offline', 'htmlhelp' and 'chmhelp' (although for now they still work if 'help_type' is unset). There is a new type, "PDF" to allow offline PDF (rather than PostScript). A function offline_help_helper() will be used if this exists in the workspace or further down the search path, otherwise the function of that name in the 'utils' name space is used. o Plain text help is now used as the fallback for HTML help (as it always was for Compiled HTML help on Windows). o It is possible to ask for static HTML pages to be prebuilt via the configure option --enable-prebuilt-html. This may be useful for those who wish to make HTML help available outside R, e.g. on a local web site. o An experimental tag \Sexpr has been added to Rd files, to evaluate expressions at build, install, or render time. Currently install time and render time evaluation are supported. o Tags \if, \ifelse and \out have been added to allow format-specific (or more general, using \Sexpr) conditional text in man pages. o The parse_Rd() parser has been made more tolerant of coding errors in Rd files: now all syntax errors are reported as warnings, and an attempt is made to continue parsing. o parse_Rd() now has an argument 'fragment' (default FALSE) to accept small fragments of Rd files (so that \Sexpr can output Rd code which is then parsed). o parse_Rd() now always converts its input to UTF-8. The Rd2* rendering functions have a new parameter, 'outputEncoding', which controls how their output is encoded. o parse_Rd() no longer includes the newline as part of a "%"-style comment. o There have been various bug fixes and code reorganization in the Rd renderers Rd2HTML, Rd2latex, Rd2txt, and Rd2ex. All example files are now created with either ASCII or UTF-8 encoding, and the encoding is only marked in the file if there is any non-UTF-8 code (previously it was marked if the help file had non-ASCII contents, possibly in other sections). o print.Rd() now adds necessary escape characters so that printing and re-parsing an Rd object should produce an equivalent object. o parse_Rd() was incorrectly handling multiple backslashes in R code strings, converting 4n+3 backslashes to 2n+1 instead of 2n+2. o parse_Rd() now recognizes the \var tag within a quoted string in R-like text. o parse_Rd() now treats the argument of \command as LaTeX-like, rather than verbatim. COMPRESSION o New function untar() to list or unpack tar archives, possibly compressed. This uses either an external 'tar' command or an internal implementation. o New function tar() to create (possibly compressed) tar archives. o New functions memCompress() and memDecompress() for in-memory compression and decompression. o bzfile() has a 'compress' argument to select the amount of effort put into compression when writing. o New function xzfile() for use with xz-compressed files. (This can also read files compressed by some versions of 'lzma'.) o gzfile() looks at the file header and so can now also read bzip2-ed files and xz-compressed files. o There are the new options of save(compress = "bzip2") and "xz" to use bzip2 or xz compression (which will be slower, but can give substantially smaller files). Argument compression_level gives finer control over the space/time tradeoffs. load() can read such saves (but only as from this version of R). o R CMD INSTALL/check and tools::writePACKAGES accept a wider range of compressed tar archives. Precisely how wide depends on the capabilities of the host system's 'tar' command: they almost always include .tar.bz2 archives, and with modern versions of 'tar' other forms of compression such as lzma and xz, and arbitrary extensions. o R CMD INSTALL has a new option --data-compress to control the compression used when lazy-loading data. New possibilities are --data-compress=bzip2 which will give ca 15% better compression at the expense of slower installation times, and --data-compress=xz, often giving even better compression on large datasets at the expense of much longer installation times. (The latter is used for the recommended packages: it is particularly effective for 'survival'.) o file() for open = "", "r" or "rt" will automagically detect compressed files (from gzip, bzip2 or xz). This means that compressed files can be specified by file name (rather than via a gzfile() connection) to read.table(), readlines(), scan() and so on. o data() can handle compressed text files with extensions .{txt,tab,csv}.{gz,bz2,xz} . DEPRECATED & DEFUNCT o png(type="cairo1") is defunct: the value is no longer recognized. o tools::Rd_parse() is defunct (as this version of R uses only Rd version 2). o Use of ~/.Rconf (which was deprecated in favour of ~/.Rconfig in 2004) has finally been removed. o Bundles of packages are deprecated. See 'Writing R Extensions' for the steps needed to unbundle a bundle. o help() arguments 'offline', 'htmlhelp' and 'chmhelp' are deprecated in favour of 'help_type'. o clearNames() ('stats') is deprecated for unname(). o Basic regular expressions (extended = FALSE) are deprecated in strsplit, grep and friends. There is a precise POSIX standard for them, but it is not what recent RE engines implement, and it seems that in almost all cases package authors intended fixed = TRUE when using extended = FALSE. o methods::trySilent() is deprecated for try(*, silent=TRUE) or - more efficiently and flexibly - something like tryCatch(*, error = function(e) e). o index.search() is deprecated: there are no longer directories of types other than 'help'. INSTALLATION o cairo >= 1.2 is now required (1.2.0 was released in July 2006) for cairo-based graphics devices (which remain optional). o A suitable iconv() is now required: support for configure option --without-iconv has been withdrawn (it was deprecated in R 2.5.0). o Perl is no longer 'essential'. R can be built without it, but scripts R CMD build, check, Rprof and Sd2d require it. o A system 'glob' function is now essential (a working Sys.glob() has been assumed since R 2.9.0 at least). o C99 support for MBCS is now required, and configure option --disable-mbcs has been withdrawn. o Having a version of 'tar' capable of automagically detecting compressed archives is useful for utils::untar(), and so 'gtar' (a common name for GNU tar) is preferred to 'tar': set environment variable TAR to specify a particular 'tar' command. INTERNATIONALIZATION o There is some makefile support for adding/updating translations in packages: see po/README and 'Writing R Extensions'. There is support for the use of 'dngettext' for C-level translations in packages: see 'Writing R Extensions'. BUG FIXES o Assigning an extra 0-length column to a data frame by DF[, "foo"] <- value now works in most cases (by filling with NAs) or fails. (It used to give a corrupt data frame.) o validObject() avoids an error during evaluation in the case of various incorrect slot definitions. o n:m now returns a result of type "integer" in a few more boundary cases. o The 'zap.ind' argument to printCoefmat() did not usually work as other code attempted to ensure that non-zero values had a non-zero representation. o printCoefmat() formatted groups of columns together, not just the cs.ind group but also the zap.ind group and a residual group. It now formats all columns except the cs.ind group separately (and zaps the zap.ind group column-by-column). The main effect will be see in the output from print.anova, as this grouped SS-like columns in the zap.ind group. o R_ReplDLLinit() initializes the top-level jump so that some embedded applications on Windows no longer crash on error. o identical() failed to take the encoding of character strings into account, so identical byte patterns are not necessarily identical strings, and similarly Latin-1 and UTF-8 versions of the same string differ in byte pattern. o methods(f) used to warn unnecessarily for an S4 generic 'f' which had been created based on an existing S3 generic. o The check for consistent ordering of superclasses was not ignoring all conditional relations (the symptom was usually spurious warnings for classes extending "array"). o Trying to assign into a raw vector with an index vector containing NAs could cause a segfault. Reported by Herv? Pag?s. o Rscript could segfault if (by user error) its filename argument was missing. Reported by Martin Morgan. o getAnywhere() (and functions that use it, including argument completion in the console) did not handle special built-in functions. Reported by Romain Francois. o order() was missing a PROTECT() call and so could segfault when called on character data under certain (rare) circumstances involving marked non-native encodings. o prettyNum(z, drop0trailing=TRUE) did not work correctly when z was a complex vector. Consequently, str(z, ...) also did not. (PR#13985) o 'make distclean' removed too many files in etc/ if builddir = srcdir. o R CMD replaced TEXINPUTS rather than appending to it (as documented and intended). o help.start() no longer fails on unix when "browser" is a function. o pbeta(x, *, log.p = TRUE) is sometimes more accurate, e.g., for very small x. o Unserializing a pre-2.8 workspace containing pure ASCII character objects with a LATIN1 or UTF-8 encoding would corrupt the CHARSXP cache. -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 From P.Dalgaard at biostat.ku.dk Tue Dec 1 11:53:16 2009 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Tue, 01 Dec 2009 11:53:16 +0100 Subject: R 2.10.1 Scheduled for December 14, 2009 Message-ID: <4B14F59C.1020201@biostat.ku.dk> This is to announce that we plan to release R version 2.10.1 on Monday, December 14, 2009. Release procedures start Friday, December 4. Those directly involved should review the generic schedule at http://developer.r-project.org/release-checklist.html The source tarballs will be made available daily (barring build troubles) and the tarballs can be picked up at http://cran.r-project.org/src/base-prerelease/ a little later. Binary builds are expected to appear starting Monday, December 7 at the latest. For the Core Team Peter Dalgaard -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 From P.Dalgaard at biostat.ku.dk Mon Dec 14 11:20:20 2009 From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard) Date: Mon, 14 Dec 2009 11:20:20 +0100 Subject: R 2.10.1 is released Message-ID: <4B261164.6070008@biostat.ku.dk> R-2.10.1.tar.gz was built a short while ago. This is a maintenance release and fixes a number of mostly minor issues. See the full list of changes below. You can get it from http://cran.r-project.org/src/base/R-2/R-2.10.1.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: 70447ae7f2c35233d3065b004aa4f331 INSTALL 433182754c05c2cf7a04ad0da474a1d0 README 4f004de59e24a52d0f500063b4603bcb OONEWS ff4bd9073ef440b1eb43b1428ce96872 ONEWS 08687cc1d9e5bb23875c1182f9f9cb2d NEWS d80a5c5808f038b36f79d8f0defaa0b9 THANKS 070cca21d9f8a6af15f992edb47a24d5 AUTHORS a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB eb723b61539feef013de476e68b5c50a COPYING 020479f381d5f9038dcb18708997f5da RESOURCES 4219bfcf875f995b84e5aebb1e02f3a5 FAQ 75f8b7e875b846ea96a4c6cc0abc00a4 R-2.10.1.tar.gz 75f8b7e875b846ea96a4c6cc0abc00a4 R-latest.tar.gz Here is the relevant part of the NEWS file: CHANGES IN R VERSION 2.10.1 NEW FEATURES o The PCRE library has been updated to version 8.00. o R CMD INSTALL has new options --no-R, --no-libs, --no-data, --no-help, --no-demo, --no-exec, and --no-inst to suppress installation of the specified part of the package. These are intended for special purposes (e.g. building a database of help pages without fully installing all packages). o The documented line-length limit of 4095 bytes when reading from the console now also applies also to parse(file="") (which previously had a limit of around 1024 bytes). o A Bioconductor mirror can be set for use by setRepositories() via the option "BioC_mirror", e.g. the European mirror can be selected by options(BioC_mirror="http://bioconductor.statistik.tu-dortmund.de") o Double-clicking in a tk_select.list() list box now selects the item and closes the list box (as happens on the Windows select.list() widget). INSTALLATION o configure will be able to find a usable libtiff in some rare circumstances where it did not previously (where libtiff needed to be linked explicitly against -ljpeg). o Making refman.pdf works around a problem with the indexing with hyperref 6.79d and later. DEPRECATED & DEFUNCT o The 'extended' argument is deprecated in strsplit(), grep(), grepl(), sub(), gsub(), regexpr() and gregexpr() (not just the value extended = FALSE) and will be removed in R 2.11.0. BUG FIXES o trigamma(x) and other psigamma(x, n) calls are now accurate for very large abs(x). (PR#14020) o [g]sub(perl=FALSE, fixed=FALSE) could use excessive stack space when used with a very long vector containing some non-ASCII strings. o The default method of weighted.mean(na.rm = TRUE) did not omit weights for NA observations in 2.10.0. (PR#14032) o [g]regexpr(pattern, fixed = TRUE) returned match positions in bytes (not characters) in an MBCS locale if 'pattern' was a single byte. [g]sub(fixed = TRUE) with a single-byte pattern could conceivably have matched part of a multibyte character in a non-UTF-8 MBCS. o findLineNum() and setBreakpoint() would sometimes fail if the specified file was not in the current directory. o Package tcltk's demo(tkdensity) was broken in 2.9.0 when demo() was changed to set par(ask = TRUE). o gsub() with backrefs could fail on extremely long strings (hundreds of thousands of characters) due to integer overflow in a length calculation. o abline(*, untf=TRUE) now uses a better x-grid in log-scale, e.g., for plot(c(1,300), c(1,300), log="xy") ; abline(4,1, untf=TRUE). o detach/unloadNamespace() arrange to flush the package's lazyload cache of R objects once the package/namespace is no longer needed. o There have been small fixes to the rendering of help, e.g. \command is now rendered verbatim (so e.g. -- is not interpreted, PR#14045). Also, there are many small changes to help files where the new converters were not rendering them in the same way as before. o available.packages() would fail when run on a repository with no packages meeting the filtering conditions. (PR#14042) o rep(x, times, each = 2) gave invalid results when the 'times' argument is a vector longer than 'x'. Reported by Bill Dunlap. o An error when unloadNamespace() attempted to run the .onUnload() function gave an error in the reporting function and so was not reported properly. o Text help rendering did not handle very long input lines properly. o promptMethods() generated signature documentation improperly. o pgamma(x, a, lower.tail=FALSE) and qgamma(..) are now considerably more accurate in some regions for very small 'a'. qgamma() now correctly returns 0 instead of NaN in similar extreme cases, and qgamma() no longer warns in the case of small 'a', see (PR#12324). o unname() now also removes names from a zero length vector. o Printing results from ls.str() no longer evaluates unevaluated calls. o complete.cases() failed on a 0-column data frame argument. (Underlies PR#14066.) It could return nonsensical results if no input determined the number of cases (seen in the no-segfault tests). o An error in nls() with a long formula could cause a segfault. (PR#14059) o qchisq(p, df, ncp, lower.tail = FALSE) with ncp >= 80 was inaccurate for small p (as the help page said): it is now less inaccurate. (In part, PR#13999.) For ncp less than but close to 80, pchisq() and qchisq() are more accurate for probablilities very close to 1 (a series expansion was truncated slightly too early). pchisq(x, df, ncp) can no longer return values just larger than one for large values of ncp. o intToUtf8() could fail when asked to produce 10Mb or more strings, something it was never intended to do: unfortunately Windows crashed R (other OSes reported a lack of resources). (PR#14068) o chisq.test() could fail when given argument 'x' or 'y' which deparsed to more than one line. (Reported by Laurent Gauthier.) o S4 methods are uncached whenever the name space containing them is unloaded (by unloadNamespace() as well as by detach(unload = TRUE)). o The internal record-keeping by dyn.load/dyn.unload was incomplete, which could crash R if a DLL that registered .External routines had earlier been unloaded. o bessel[JY](x, nu) with nu a negative integer (a singular case) is now correct, analogously to besselI(), see PR#13556, below. o tools::file_path_as_absolute() doubled the file separator when applied to a file such as "/vmunix" or (on Windows) "d:/afile" in a directory for which getwd() would return a path with a trailing separator (largely cosmetic, as reasonable file systems handle such a path correctly). (Perhaps what was meant by PR#14078.) o unsplit(drop = TRUE) applied to a data frame failed to pass 'drop' to the computation of row names. (PR#14084) o The "difftime" method of mean() ignored its 'na.rm' argument. o tcltk::tk_select.list() is now more likely to remove the widget immediately after selection is complete. o Adding/subtracting a "difftime" object to/from a "POSIXt" or "Date" object works again (it was broken by the addition of Ops.difftime). o Conversion to latex of an Rd file with no aliases failed. o wilcox.test(*, conf.int=TRUE) has achieved.level corrected and, for exact=FALSE, now gives an 'estimate' which does not depend on the alternative used. o help.search() failed when the package argument was specified. (PR#14113) o switch(EXPR = "A") now returns NULL, as switch(1) {which used to signal an error}. -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907